R3D Align: Global Pairwise Alignment of RNA 3D Structures Using Local Superpositions

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2010 Oct 9

PMID 20929913

Citations 30

Authors

Ryan R Rahrig

Neocles B Leontis

Craig L Zirbel

Affiliations

Soon will be listed here.

Abstract

Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the 'local alignment' graph.

Results: The algorithm is implemented in a program suite and web server called 'R3D Align'. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments.

Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location.

Citing Articles

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A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.

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Context-sensitivity of isosteric substitutions of non-Watson-Crick basepairs in recurrent RNA 3D motifs.

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LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.

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References

Krasilnikov A, Xiao Y, Pan T, Mondragon A . Basis for structural diversity in homologous RNAs. Science. 2004; 306(5693):104-7. DOI: 10.1126/science.1101489. View

Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H . Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 2003; 31(13):3450-60. PMC: 168936. DOI: 10.1093/nar/gkg529. View

Olson W . Configurational statistics of polynucleotide chains. A single virtual bond treatment. Macromolecules. 1975; 8(3):272-5. DOI: 10.1021/ma60045a006. View

Duarte C, Wadley L, Pyle A . RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Res. 2003; 31(16):4755-61. PMC: 169959. DOI: 10.1093/nar/gkg682. View

Capriotti E, Marti-Renom M . RNA structure alignment by a unit-vector approach. Bioinformatics. 2008; 24(16):i112-8. DOI: 10.1093/bioinformatics/btn288. View

Chang Y, Huang Y, Lu C . SARSA: a web tool for structural alignment of RNA using a structural alphabet. Nucleic Acids Res. 2008; 36(Web Server issue):W19-24. PMC: 2447761. DOI: 10.1093/nar/gkn327. View

Berman H, Battistuz T, Bhat T, Bluhm W, Bourne P, Burkhardt K . The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2002; 58(Pt 6 No 1):899-907. DOI: 10.1107/s0907444902003451. View

Ferre F, Ponty Y, Lorenz W, Clote P . DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. Nucleic Acids Res. 2007; 35(Web Server issue):W659-68. PMC: 1933154. DOI: 10.1093/nar/gkm334. View

Sarver M, Zirbel C, Stombaugh J, Mokdad A, Leontis N . FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol. 2007; 56(1-2):215-52. PMC: 2837920. DOI: 10.1007/s00285-007-0110-x. View

10.

Hershkovitz E, Tannenbaum E, Howerton S, Sheth A, Tannenbaum A, Williams L . Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA. Nucleic Acids Res. 2003; 31(21):6249-57. PMC: 275477. DOI: 10.1093/nar/gkg835. View

11.

Selmer M, Dunham C, Murphy 4th F, Weixlbaumer A, Petry S, Kelley A . Structure of the 70S ribosome complexed with mRNA and tRNA. Science. 2006; 313(5795):1935-42. DOI: 10.1126/science.1131127. View

12.

Wimberly B, Brodersen D, Clemons Jr W, Morgan-Warren R, Carter A, Vonrhein C . Structure of the 30S ribosomal subunit. Nature. 2000; 407(6802):327-39. DOI: 10.1038/35030006. View

13.

Schuwirth B, Borovinskaya M, Hau C, Zhang W, Vila-Sanjurjo A, Holton J . Structures of the bacterial ribosome at 3.5 A resolution. Science. 2005; 310(5749):827-34. DOI: 10.1126/science.1117230. View

14.

Klein D, Moore P, Steitz T . The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J Mol Biol. 2004; 340(1):141-77. DOI: 10.1016/j.jmb.2004.03.076. View

15.

Stombaugh J, Zirbel C, Westhof E, Leontis N . Frequency and isostericity of RNA base pairs. Nucleic Acids Res. 2009; 37(7):2294-312. PMC: 2673412. DOI: 10.1093/nar/gkp011. View

16.

Ortiz A, Strauss C, Olmea O . MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci. 2002; 11(11):2606-21. PMC: 2373724. DOI: 10.1110/ps.0215902. View

17.

NEEDLEMAN S, Wunsch C . A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970; 48(3):443-53. DOI: 10.1016/0022-2836(70)90057-4. View

18.

Zirbel C, Sponer J, Sponer J, Stombaugh J, Leontis N . Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res. 2009; 37(15):4898-918. PMC: 2731888. DOI: 10.1093/nar/gkp468. View

19.

Krasilnikov A, Yang X, Pan T, Mondragon A . Crystal structure of the specificity domain of ribonuclease P. Nature. 2003; 421(6924):760-4. DOI: 10.1038/nature01386. View

20.

Dror O, Nussinov R, Wolfson H . ARTS: alignment of RNA tertiary structures. Bioinformatics. 2005; 21 Suppl 2:ii47-53. DOI: 10.1093/bioinformatics/bti1108. View